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TreeTools (version 1.7.3)

Create, Modify and Analyse Phylogenetic Trees

Description

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) ; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) , and of tree balance (Mir et al. 2013) ; artificial extinction (Asher & Smith, 2022) ; import and export of trees from Newick, Nexus (Maddison et al. 1997) , and TNT formats; and analysis of splits and cladistic information.

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Install

install.packages('TreeTools')

Monthly Downloads

1,996

Version

1.7.3

License

GPL (>= 3)

Issues

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Repository

https://github.com/ms609/TreeTools/

Homepage

https://ms609.github.io/TreeTools/

Maintainer

Martin R. Smith

Last Published

July 20th, 2022

Functions in TreeTools (1.7.3)

Convert phylogenetic tree to ClusterTable

ArtificialExtinction

Artificial Extinction

ClusterTable-methods

S3 methods for ClusterTable objects

Collapse nodes on a phylogenetic tree

Add full stop to end of a sentence

Distance between edges

DescendantEdges

Identify descendant edges

DoubleFactorial

Double factorial

Construct consensus trees

CompatibleSplits

Which splits are compatible?

Drop leaves from tree

Ancestors of an edge

Identify vertices retained when leaves are dropped

Generate a neighbour joining tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of distinct splits

Number of trees

ConsensusWithout

Reduced consensus, omitting specified taxa

Generate pectinate, balanced or random trees

LeafLabelInterchange

Leaf label interchange

Convert between matrices and phyDat objects

EnforceOutgroup

Generate a tree with a specified outgroup

Constrained neighbour-joining tree

Extract taxa from a matrix block

Data from Zhang et al. 2016

Hamming distance between taxa in a phylogenetic dataset

Count descendants for each node in a tree

Calculate length of paths between each pair of vertices within tree

PairwiseDistances

Distances between each pair of trees

Number of trees one SPR step away

Most recent common ancestor

Renumber a tree's nodes and tips

Renumber a tree's tips

Which node is a tree's root?

Visualize position of rogue taxa

Reorder edges of a phylogenetic tree

Distance of each node from tree exterior

MorphoBankDecode

Decode MorphoBank text

Order of each node in a tree

Convert between strings and phyDat objects

Polarize splits on a single taxon

NonDuplicateRoot

Non-duplicate root

Convert object to Splits

SingleTaxonTree

Generate a single taxon tree

Read phylogenetic characters from file

Unique integer indices for bifurcating tree topologies

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Add tree to start of list

TotalCopheneticIndex

Total Cophenetic Index

WriteTntCharacters

Write morphological character matrix to TNT file

Is tree rooted?

Root or unroot a phylogenetic tree

ImposeConstraint

Force a tree to match a constraint

Reorder tree edges and nodes

RightmostCharacter

Rightmost character of string

logDoubleFactorials

Natural logarithms of double factorials

'Stemwardness' of a leaf

Subset of a split on fewer leaves

TreeTools-package

Paths present in reduced tree

Integer representing shape of a tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

SplitMatchProbability

Probability of matching this well

Write a phylogenetic tree in Newick format

doubleFactorials

Double factorials

TreesMatchingSplit

Number of trees matching a bipartition split

Efficiently convert edge matrix to splits

Generate binary tree by collapsing polytomies

Minimum spanning tree

Number of leaves in a phylogenetic tree

TreesMatchingTree

Number of trees containing a tree

Extract tip labels

Tips contained within splits

Write Newick Tree

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

Identify and remove trivial splits

Convert object to multiPhylo class

sort.multiPhylo

Sort a list of phylogenetic trees

Apply a function that returns 64-bit integers over a list or vector

Produce a legend for continuous gradient scales

Random parent vector

Frequency of splits

Brewer palettes

Colour for node support value

Extract a subtree

Number of rooted / unrooted tree shapes

Exclusive OR operation

print.TreeNumber

Print TreeNumber object

CharacterInformation

Character information content

Read modification time from "ape" Nexus file

Cladistic information content of a tree

Add a tip to a phylogenetic tree